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The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture. [ABSTRACT FROM AUTHOR]

In human microbiome studies, mediation analysis has recently been spotlighted as a practical and powerful analytic tool to survey the causal roles of the microbiome as a mediator to explain the observed relationships between a medical treatment/environmental exposure and a human disease. We also note that, in a clinical research, investigators often trace disease progression sequentially in time; as such, time-to-event (e.g., time-to-disease, time-to-cure) responses, known as survival responses, are prevalent as a surrogate variable for human health or disease. In this paper, we introduce a web cloud computing platform, named as microbiome mediation analysis with survival responses (MiMedSurv), for comprehensive microbiome mediation analysis with survival responses on user-friendly web environments. MiMedSurv is an extension of our prior web cloud computing platform, named as microbiome mediation analysis (MiMed), for survival responses. The two main features that are well-distinguished are as follows. First, MiMedSurv conducts some baseline exploratory non-mediational survival analysis, not involving microbiome, to survey the disparity in survival response between medical treatments/environmental exposures. Then, MiMedSurv identifies the mediating roles of the microbiome in various aspects: (i) as a microbial ecosystem using ecological indices (e.g., alpha and beta diversity indices) and (ii) as individual microbial taxa in various hierarchies (e.g., phyla, classes, orders, families, genera, species). To illustrate its use, we survey the mediating roles of the gut microbiome between antibiotic treatment and time-to-type 1 diabetes. MiMedSurv is freely available on our web server (http://mimedsurv.micloud.kr). [ABSTRACT FROM AUTHOR]

Bacterial culturomics is a set of techniques to isolate and identify live bacteria from complex microbial ecosystems. Despite its potential to revolutionize microbiome research, bacterial culturomics has significant challenges when applied to human gut microbiome studies due to its labor-intensive nature. Therefore, we established a streamlined culturomics approach with minimal culture conditions for stool sample preincubation. We evaluated the suitability of non-selective medium candidates for maintaining microbial diversity during a 30-day incubation period based on 16S rRNA gene amplicon analysis. Subsequently, we applied four culture conditions (two preincubation media under an aerobic/anaerobic atmosphere) to isolate gut bacteria on a large scale from eight stool samples of healthy humans. We identified 8141 isolates, classified into 263 bacterial species, including 12 novel species candidates. Our analysis of cultivation efficiency revealed that seven days of aerobic and ten days of anaerobic incubation captured approximately 91% and 95% of the identified species within each condition, respectively, with a synergistic effect confirmed when selected preincubation media were combined. Moreover, our culturomics findings expanded the coverage of gut microbial diversity compared to 16S rRNA gene amplicon sequencing results. In conclusion, this study demonstrated the potential of a streamlined culturomics approach for the efficient isolation of gut bacteria from human stool samples. This approach might pave the way for the broader adoption of culturomics in human gut microbiome studies, ultimately leading to a more comprehensive understanding of this complex microbial ecosystem. [ABSTRACT FROM AUTHOR]

The present study assessed the growth and fish performance of juvenile red sea bream fed four isonitrogenous (46–48%) and isolipidic (15%) diets containing 45% fishmeal (control) and 15%, 30%, and 45% defatted black soldier fly (BSF) Hermetia illucens meal for 67 days. Subsequent analyses showed that there were no significant differences in the growth parameters, nutrient digestibility, and body composition of fish among all treatments. Although no significant difference was observed in fish growth, low growth was observed when the fish meal was totally replaced with the BSF meal. Higher alpha diversity of intestinal microbiota was observed in fish fed the BSF meal-based diet compared to that of the control. In the treatment groups fed the BSF meal, elevations in the presence of microbial genera that produce digestive enzymes, such as chitinase (Nocardia, Vibrio, Paenibacillus, Photobacterium), lipase (Paenibacillus, Photobacterium), and trypsin-like serine protease (Bacillus, Paenibacillus) and vitamin B group [biotin (Vibrio, Paenibacillus, Bacillus), cobalamin (Pseudomonas, Bacillus, Propionibacterium), and pyridoxin (Photobacterium)], were observed. We also found an increasing trend of bacteria producing antioxidative enzymes, such as superoxide dismutase and catalase (Nocardia, Pseudomonas, Photobacterium) in the BSF groups. These results suggested that the BSF meal could replace 67% of fishmeal without causing a negative impact on growth and lead to beneficial effects on the intestinal microbiota of the red sea bream. [ABSTRACT FROM AUTHOR]

Lignocellulosic biomass is of significant industrial and scientific interest. Residues derived from different activities (agro-industrial work, food consumption, wood use, urban solid waste, etc.) and their subsequent use are key to extending circularity models to the different technological sectors that are beginning to implement circular economy cycles. Biorefineries are integrated platforms that value waste conversion into various value-added products. The generation of bioproducts derived from lignocellulosic waste (green fuels, green chemicals, and biomaterials) has promoted a shift from a fossil fuel–based economy to a more sustainable one. In addition, integrating biorefineries into the circular economy framework promotes a comprehensive approach to resource management, waste reduction, and sustainable development, which contributes to the overall resilience and efficiency of societal systems. There has been increased focus on the application of "canonical microorganisms" for residual biomass conversion, such as fungi, bacteria, and yeast. However, there is a plethora of other potential microorganisms that can be candidates for new biotechnological applications. This review aims to describe the valorization of different sources of lignocellulosic biomass in the global context, with a focus on Brazilian practice, and to emphasize how the use of microbial diversity is critical to enhancing current technologies, such as advanced liquid fuels. Finally, there is a discussion of the potential of anaerobic fungi, archaea, protists, and oomycetes as microbial product conversion technologies. [ABSTRACT FROM AUTHOR]

The microbiome is intricately linked to the development of psoriasis, serving as both a potential cause and consequence of the psoriatic process. In recent years, there has been growing interest among psoriasis researchers in exploring how psoriasis treatments affect the skin and gut microbiome. However, a comprehensive evaluation of the impact of modern treatment approaches on the microbiome has yet to be conducted. In this systematic review, we analyze studies investigating alterations in the skin and gut microbiome resulting from psoriasis treatment, aiming to understand how current therapies influence the role of the microbiome in psoriasis development. The systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. PubMed and Scopus databases were searched for eligible studies from the inception dates until July 5, 2023. Study selection, data extraction, and risk of bias assessment were carried out by three overlapping pairs of reviewers, resolving any disagreements through consensus. Our analysis of various treatments, including biologics, conventional medications, phototherapy, and probiotics, reveals significant shifts in microbial diversity and abundance. Importantly, favorable treatment outcomes are associated with microbiota alterations that approach those observed in healthy individuals. While the studies reviewed exhibit varying degrees of bias, underscoring the need for further research, this review supports the potential of microbiome modulation as both a preventive and therapeutic strategy for psoriasis patients. The findings underscore the importance of personalized therapeutic approaches, recognizing the profound impact of treatment on the microbiome. They also highlight the promise of probiotics, prebiotics, and dietary interventions in psoriasis management. [ABSTRACT FROM AUTHOR]

This study was designed to recover representative culturable actinomycetes from the Atacama Desert, and to detect their ability to promote plant growth under drought conditions. Environmental samples were taken from three Atacama Desert habitats, namely, from the Aguas Calientes, Lomas Bayas and Yungay core regions. With one exception higher actinomycete counts were obtained when isolation media were inoculated with mineral particles than with corresponding aliquots of serial dilution. Comparative 16S rRNA gene sequencing showed that representative isolates belonged to thirteen genera including putative novel Blastococcus, Kocuria, Micromonospora, Pseudonocardia, Rhodococcus and Streptomyces species. Representative isolates produced indole-3-acetic acid, siderophore and solubilized phosphate as well as displaying an ability to grow under drought conditions. In conclusion, the current findings open up exciting prospects for the promising potential of actinomycetes from the Atacama Desert to be used as bioinoculants to promote plant growth in arid and semi-arid biomes. [ABSTRACT FROM AUTHOR]

Bioaerosol emitted in university biological laboratories may exert adversely effects on employees and students. The occupational health and safety have been given much importance. This study aimed to monitor the risk of bioaerosol formation inside a biological wastewater treatment laboratory where other biological activities were performed along with wastewater treatment using the biological method. The concentration of bacterial and fungal bioaerosols was studied, and the diversity of the air microbiota was evaluated, using a single-stage impactor. The purpose of the Corelation research was to evaluate the effects of indoor biological activity unique to wastewater labs and building characteristics. Increased number of occupants (corelation efficient- 0.71 and 0.47 respectively) and their experimental activity related to wastewater treatment drastically elevated both mesophiles (2018 MPN·m−3) and psychrophiles (1128 MPN·m−3) concentrations in early winter, which crossed permissible limits, whereas the fungal concentration was found below the upper permissible limits (78 MPN·m−3) in same condition. The fungal bioaerosols were found to get influenced by seasonal change and humidity (highest during autumn- 406 MPN·m−3) and were not really influenced by number of occupants (corelation efficient- 0.33). This result suggests a moderate risk of bacterial bioaerosol to occupants working in wastewater treatment laboratory. These findings may contribute to promotion and implementation of indoor environment safety at educational institute and may help in formation of policy to regulate indoor bioaerosol levels. [ABSTRACT FROM AUTHOR]

The maternal pregnancy microbiome (including genitourinary and gut) has been linked to important pregnancy/birth and later childhood health outcomes. However, such sampling as part of large population cohort studies is logistically and financially challenging. Many countries routinely collect vaginal or vaginal-rectal swabs in late pregnancy for Group B Streptococcus (GBS) screening, but their utility for population-based research is still unclear. As part of planning for the Generation Victoria population-based cohort study beginning in pregnancy, we assessed the utility and reliability of residual clinical GBS vaginal/vaginal-rectal swabs for generating late pregnancy microbiome data. We carried out a two-phased pilot study. Phase one assessed the level of microbial diversity apparent in 'residual' clinical vaginal/vaginal-rectal swabs post clinical testing and storage for 7–10 days at 4 °C (routine clinical practice). Phase two directly assessed the impact of storage time and temperature on the microbial composition of vaginal/vaginal-rectal swabs collected specifically for research purposes. The microbiota composition in the 'residual' clinical swabs aligned with published studies. The 'research' swabs, stored at 4 °C for up to ten days, showed minimal changes in microbiota profile, compared to swabs examined on the day of collection. In contrast, significant variation in diversity was seen in swabs stored at room temperature for up to 48 h. Residual clinical material from swabs collected primarily for GBS screening in late pregnancy represent a reliable and abundant source of material for assessing the late pregnancy maternal microbiome for research purposes. This represents a low-burden opportunity for population-representative pregnancy studies to assess the potential of late pregnancy microbiome for prediction and understanding maternal and child health outcomes. [ABSTRACT FROM AUTHOR]

Cigars and cigarillos are emerging as popular tobacco alternatives to cigarettes. However, these products may be equally harmful to human health than cigarettes and are associated with similar adverse health effects. We used 16S rRNA gene amplicon sequencing to extensively characterize the microbial diversity and investigate differences in microbial composition across 23 different products representing three different cigar product categories: filtered cigar, cigarillo, and large cigar. High throughput sequencing of the V4 hypervariable region of the 16 s rRNA gene revealed 2124 Operational Taxonomic Units (OTUs). Our findings showed that the three categories of cigars differed significantly in observed richness and Shannon diversity, with filtered cigars exhibiting lower diversity compared to large cigars and cigarillos. We also found a shared and unique microbiota among different product types. Firmicutes was the most abundant phylum in all product categories, followed by Actinobacteria. Among the 16 genera shared across all product types were Bacillus, Staphylococcus, Pseudomonas, and Pantoea. Nine genera were exclusively shared by large cigars and cigarillos and an additional thirteen genera were exclusive to filtered cigars. Analysis of individual cigar products showed consistent microbial composition across replicates for most large cigars and cigarillos while filtered cigars showed more inter-product variability. These findings provide important insights into the microbial diversity of the different cigar product types. [ABSTRACT FROM AUTHOR]

The kiwifruit industry typically uses commercial pollen for artificial pollination. However, during the collection of male flowers and pollen production, pollen can be easily contaminated by pathogenic bacteria that cause diseases such as canker and flower rot. Consequently, it is crucial to understand the structure of the pollen microbial community. This study employed Illumina high-throughput sequencing technology to analyze the fungal and bacterial composition in pollen samples from various regions in Shaanxi Province. Concurrently, potential pathogenic strains were isolated using traditional microbial isolation and cultivation techniques, and their molecular identification was performed through 16S rDNA sequence analysis. A tieback test was conducted on healthy branches to verify the pathogenicity of the strains. The results revealed a rich diversity of fungi and bacteria in kiwifruit pollen. At the phylum level, pollen fungi were mainly distributed in Ascomycota, and bacteria were mainly distributed in Proteobacteria and Firmicutes. The dominant fungal genera were Mycosphaerella, Aspergillus, and Cladosporium; the dominant bacterial genera were Weissella, Pantoea, Enterobacter, and Pseudomonas, respectively. Additionally, both Erwinia persicina and Pseudomonas fluorescens, isolated from pollen, exhibited high pathogenicity toward healthy kiwifruit branches. These findings contribute to a deeper understanding of the microbial diversity in commercial kiwifruit pollen used for mass pollination. [ABSTRACT FROM AUTHOR]

Polygonatum kingianum Collett & Hemsl., is one of the most important traditional Chinese medicines in China. The purpose of this study is to investigate the relationship between herb quality and microbial-soil variables, while also examining the composition and structure of the rhizosphere microbial community in Polygonatum kingianum, the ultimate goal is to provide a scientific approach to enhancing the quality of P. kingianum. Illumina NovaSeq technology unlocks comprehensive genetic variation and biological functionality through high-throughput sequencing. And in this study it was used to analyze the rhizosphere microbial communities in the soils of five P. kingianum planting areas. Conventional techniques were used to measure the organic elements, pH, and organic matter content. The active ingredient content of P. kingianum was identified by High Performance Liquid Chromatography (HPLC) and Colorimetry. A total of 12,715 bacterial and 5487 fungal Operational Taxonomic Units (OTU) were obtained and taxonomically categorized into 81 and 7 different phyla. Proteobacteria, Bacteroidetes, and Acidobacteriae were the dominant bacterial phyla Ascomycota and Basidiomycota were the dominat fungal phyla. The key predictors for bacterial community structure included hydrolysable nitrogen and available potassium, while for altering fungal community structure, soil organic carbon content (OCC), total nitrogen content (TNC), and total potassium content (TPOC) were the main influencing factors. Bryobacter and Candidatus Solibacter may indirectly increase the polysaccharide content of P. kingianum, and can be developed as potential Plant Growth Promoting Rhizobacteria (PGPR). This study has confirmed the differences in the soil and microorganisms of different origins of P. kingianum, and their close association with its active ingredients. And it also broadens the idea of studying the link between plants and microorganisms. [ABSTRACT FROM AUTHOR]

In recent years, microbial inoculants have showed a great potential to replace chemical fertilizers as a new generation of soil amendment agents, however, the understanding of their effects on nutrient cycling within plants and rhizosphere microbial diversity are still limited. In this study, the rhizosphere growth-promoting bacteria MQB12 was used to inoculate Vigna radiata to evaluate the effects of external inoculants on plant transcriptomics and rhizosphere soil microbial diversity. Enrichment analysis using GO and KEGG revealed significant enrichment in DNA-binding transcription factor activity, transcriptional regulatory factor activity, and phenylpropanoid biosynthesis among the differentially expressed genes. MQB12 inoculation positively responded to phosphorus starvation response, increased the expression of phosphorus starvation response genes (PHT/PAP), enhanced the synthesis of ethylene and salicylic acid to cope with external stress, and improved the expression of plant disease resistance genes to strengthen the disease resistance of plants to pathogens. At the same time, microbial diversity analysis further revealed the positive effect of MQB12 inoculum. MQB12 inoculum enriched beneficial flora, improved flora abundance, changed the structure and diversity of V. radiata rhizosphere microbial community, enhanced the interconnections between the flora, and positively promoted growth. MQB12 was found to adjust the microflora of the rhizosphere, which subsequently changed the environment for plant colonization. This change led to the enrichment of beneficial bacteria and removal of pathogenic bacteria, which positively affected the internal pathways of plants. Additionally, changes in gene expression levels of plants resulted in the formation of different phenotypes and various metabolites, further influencing the formation of rhizosphere microbial communities through close contact between roots and soil. This study provides new insights into the effects of microbial agents on plant growth and root environment construction and is conducive to the further development and application of microbial agents. [ABSTRACT FROM AUTHOR]

Vermicomposting utilizes the synergistic effect of earthworms with microorganisms to accelerate the stabilization of organic matter in biowastes. Nevertheless, the exact mechanism behind the maturity of vermicompost and the growth of earthworms exposed to biochar of varying particle sizes remains unclear. This study presents an investigation of the effect of biochar particle size on earthworm (Eisenia fetida) survival, microbial diversity, and the quality of vermicompost products. To address these issues, pelletized dewatered sludge samples from a municipal sewage treatment plant were amended with pine-based biochar with particle sizes of 1–2 mm, 25–75 μm, 200 nm, and 60 nm as the substrate for vermicomposting. This study revealed that the addition of millimeter-scale biochar and micron-scale biochar significantly promoted the degradation of organic matter since the organic matter in the treatment with 1–2 mm biochar at the end of the vermicomposting experiment decreased by 12.6%, which was equivalent to a 1.9-fold increase compared with that of the control. Excessive nanopowdering of nanobiochar significantly affected the survival of earthworms and led to 24.4–33.3% cumulative mortality, while millimeter-scale (mm) biochar and micron-scale (μm) biochar achieved zero mortality. The findings of this study could be used for evaluating the potential impact of nanoscale biochar to earthworms and guiding biochar-augmented vermicomposting. Highlights: The addition of 1–2 mm biochar resulted in a 1.9-fold greater reduction in organic matter compared to the control group. The introduction of 25–75 μm biochar led to a significant 94% increase in earthworm cocoons. The cumulative mortality rates of 200 nm and 60 nm biochar amendment reached peaks of 33.3% and 24.4% at first week, respectively. Earthworms excrete mucus that effectively removes attached nanobiochar. [ABSTRACT FROM AUTHOR]

There is a significant focus on the role of the host microbiome in different outcomes of human parasitic diseases, including cystic echinococcosis (CE). This study was conducted to identify the intestinal microbiome of patients with CE at different stages of hydatid cyst compared to healthy individuals. Stool samples from CE patients as well as healthy individuals were collected. The samples were divided into three groups representing various stages of hepatic hydatid cyst: active (CE1 and CE2), transitional (CE3), and inactive (CE4 and CE5). One family member from each group was selected to serve as a control. The gut microbiome of patients with different stages of hydatid cysts was investigated using metagenomic next-generation amplicon sequencing of the V3–V4 region of the 16S rRNA gene. In this study, we identified 4862 Operational Taxonomic Units from three stages of hydatid cysts in CE patients and healthy individuals with a combined frequency of 2,955,291. The most abundant genera observed in all the subjects were Blautia, Agathobacter, Faecalibacterium, Bacteroides, Bifidobacterium, and Prevotella. The highest microbial frequency was related to inactive forms of CE, and the lowest frequency was observed in the group with active forms. However, the lowest OTU diversity was found in patients with inactive cysts compared with those with active and transitional cyst stages. The genus Agatobacter had the highest OTU frequency. Pseudomonas, Gemella, and Ligilactobacillus showed significant differences among the patients with different stages of hydatid cysts. Additionally, Anaerostipes and Candidatus showed significantly different reads in CE patients compared to healthy individuals. Our findings indicate that several bacterial genera can play a role in the fate of hydatid cysts in patients at different stages of the disease. [ABSTRACT FROM AUTHOR]

Manipulating the rhizosphere microbiome to enhance plant stress tolerance is an environmentally friendly technology and a renewable resource to restore degraded environments. Here we suggest a sustainable bioremediation strategy on the example of Stebnyk mine tailings storage. We consider Salicornia europaea rhizosphere community, and the ability of the phytoremediation plant Salix viminalis to recruit its beneficial microbiome to mediate the pollution stress at the Stebnyk mine tailings storage. The tailings contain large amounts of brine salts and heavy metals that contaminate the ground water and surrounding areas, changing soil biogeochemistry and causing increased erosion. The species richness of the endophytic bacterial community of S. viminalis roots was assessed based on observed OTUs, Shannon-InvSimpson, and evenness index. Our results obtained using the plant-based enrichment strategy show that biodiversity was decreased across the contamination zones and that S. europaea supplementation significantly increased the species richness. Our results also indicate that the number of dominating bacteria was not changed across zones in both S. europaea-treated and untreated bacterial populations, and that the decrease in richness was mainly caused by the low abundant bacterial OTUs. The importance of selecting the bioremediation strains that are likely to harbor a reservoir of genetic traits that aid in bioremediation function from the target environment is discussed [ABSTRACT FROM AUTHOR]

Background: Sugarcane red rot is a soil-borne disease caused by Colletotrichum falcatum. It can reduce the yield of sugarcane and the purity of sugarcane juice, which seriously restricts the development of sucrose industry. Biocontrol bacteria can control diseases by regulating rhizosphere microecology. In this study, the effects of biocontrol bacteria on sugarcane rhizosphere microecology were studied by metagenomics and metabolomics, and the control effects of biocontrol bacteria and rhizosphere dominant bacteria on sugarcane red rot were further explored by pot experiment. Results: The results of metagenomic sequencing showed that inoculation with B. velezensis YC89 and pathogens could significantly change the microbial diversity of the sugarcane rhizosphere. The relative abundance of beneficial strains such as Streptomyces, Burkholderia, Sphingomonas, and Rhizobium increased significantly in the rhizosphere of sugarcane in the YC treatment group. Pseudomonas was significantly enriched in the rhizosphere of sugarcane in the C treatment group. The results of metabolome sequencing showed that the content of amino acids in sugarcane root exudates increased after inoculation with B. velezensis YC89, and the contents of phenolic acids and flavonoids decreased. Spearman correlation analysis showed that there was a significant correlation between differential metabolites and rhizosphere microorganisms. The results of pot experiment showed that YC89 strain and three rhizosphere microorganisms could significantly reduce the disease index of red rot and promote the growth of sugarcane plants. In addition, these strains can also significantly increase the JA and SA content of sugarcane leaves and induce plant system resistance-related enzyme activities. Among them, the synthetic community treatment group had the best biocontrol effect on red rot, and its relative control effect was 67.50%. Conclusions: Therefore, we conclude that B. velezensis YC89 could recruit beneficial rhizosphere microorganisms to enrich the rhizosphere and change the content of some phenolic acids and flavonoids in the root exudates. In addition, the isolated rhizosphere dominant bacteria and YC89 strain can resist red rot by inducing plant systemic resistance and promote the growth of sugarcane plants. This study provides a theoretical basis for the use of biocontrol bacteria to regulate rhizosphere bacteria to jointly control plant soil-borne diseases. [ABSTRACT FROM AUTHOR]

Monoculture cultivation patterns in agro-ecosystems only provide less varied soil organic matter (SOM) molecules of plant origin. Whether and how the natural fallow stage between cultivation seasons facilitates the restoration of SOM molecular diversity and mitigates the adverse impacts of constant cropping pattern is elusive. Here, we utilized FT-ICR-MS, UHPLC-MS/MS, and high-throughput sequencing to investigate the biological change processes in SOM molecular composition under cultivation and fallow status in a long-farmed paddy field. Our study showed that SOM molecular diversity increased by 45.70%–85.36% in fallow stage compared to rice cultivation season. SOM molecular diversity was positively correlated with bacterial diversity and root exudate molecular diversity, and negatively correlated with fungal diversity. Notably, root exudate molecular diversity accounted for 48.48% of the variation in SOM molecular diversity. The increased SOM molecular diversity in fallow stage was attributed more to the diverse plant-produced molecules than the microbe-consumed molecules. Plant species turnover resulted in the conversion of root exudate components to Organoheterocyclic compounds and Organic acids/derivatives from rice planting stage to fallow stage. Recruited microbes were dominated by Basidiomycita, Ascomycota, Acidobacteria, Chloroflexi and Proteobacteria, resulting in the transformation from carbohydrates, lipid-like SOM molecules to lipid-like and lignin-like SOM molecules. Both field and microcosm experiments confirmed that root exudates are the main source of SOM molecules, and are influenced by the soil microbial community. This study provides solid evidence that fallow status in agro-ecosystems provides explosion of biodiversity and counteracts the negative effects of long-term monoculture cultivation on SOM diversity. Highlights: • Natural fallow promotes soil organic matter molecular diversity in paddy fields. • Plant diversity and bacterial diversity increase in fallow stage. • Root exudates increase SOM molecular diversity by mediating microbial communities. • Variations in the composition of biological communities drive transformations in SOM molecular composition. [ABSTRACT FROM AUTHOR]

The Eastern Pamir, distinguished with high altitude, extremely arid and cold climate, limited nutrients and sparse vegetation, is a unique ecological reservoir. Microbial communities play a central role in maintaining Eastern Pamir's ecosystem functioning. Despite the ecological significance, due to the difficulty of sample collection and microbial isolation, the microbial diversity and its functionality at the Pamir Plateau have been rarely documented. To fill this gap, 80 soil samples from 17 sites across different elevations were collected, performed the rDNA amplicon sequencing to present the first large-scale overview of bacterial, archaeal, and fungal communities in the Eastern Pamir. Microbiome analysis revealed that the bacteria Actinobacteria, Alphaproteobacteria and Bacteroidia, alongside such as archaea Nitrososphaeria and Halobacteria, and fungi including Dothideomycetes, Sordariomycetes and Eurotiomycetes were dominant lineages at class level in soil microbial communities. The community structure and biodiversity of soil microorganisms provided by this dataset would be pivotal for future studies aimed at understanding the biogeographical distribution, ecological functions and environmental responses of microbial communities of the Pamir Plateau. [ABSTRACT FROM AUTHOR]

Plants thrive in diverse environments, where root-microbe interactions play a pivotal role. Date palm (Phoenix dactylifera L.), with its genetic diversity and resilience, is an ideal model for studying microbial adaptation to different genotypes and stresses. This study aimed to analyze the bacterial and fungal communities associated with traditional date palm cultivars and the widely cultivated "Deglet Nour" were explored using metabarcoding approaches. The microbial diversity analysis identified a rich community with 13,189 bacterial and 6442 fungal Amplicon Sequence Variants (ASVs). Actinobacteriota, Proteobacteria, and Bacteroidota dominated bacterial communities, while Ascomycota dominated fungal communities. Analysis of the microbial community revealed the emergence of two distinct clusters correlating with specific date palm cultivars, but fungal communities showed higher sensitivity to date palm genotype variations compared to bacterial communities. The commercial cultivar "Deglet Nour" exhibited a unique microbial composition enriched in pathogenic fungal taxa, which was correlated with its genetic distance. Overall, our study contributes to understanding the complex interactions between date palm genotypes and soil microbiota, highlighting the genotype role in microbial community structure, particularly among fungi. These findings suggest correlations between date palm genotype, stress tolerance, and microbial assembly, with implications for plant health and resilience. Further research is needed to elucidate genotype-specific microbial interactions and their role in enhancing plant resilience to environmental stresses. [ABSTRACT FROM AUTHOR]

Introduction: Microbial communities affect several aspects of the earth's ecosystem through their metabolic interaction. The dynamics of this interaction emerge from complex multilevel networks of crosstalk. Elucidation of this interaction could help us to maintain the balance for a sustainable future. Objectives: To investigate the chemical language among highly abundant microbial genera in the rhizospheres of medicinal plants based on the metabolomic analysis at the interaction level. Methods: Coculturing experiments involving three microbial species: Aspergillus (A), Trichoderma (T), and Bacillus (B), representing fungi (A, T) and bacteria (B), respectively. These experiments encompassed various interaction levels, including dual cultures (AB, AT, TB) and triple cultures (ATB). Metabolic profiling by LC-QTOFMS revealed the effect of interaction level on the productivity and diversity of microbial specialized metabolites. Results: The ATB interaction had the richest profile, while the bacterial profile in the monoculture condition had the lowest. Two native compounds of the Aspergillus genus, aspergillic acid and the dipeptide asperopiperazine B, exhibited decreased levels in the presence of the AT interaction and were undetectable in the presence of bacteria during the interaction. Trichodermarin N and Trichodermatide D isolated from Trichoderma species exclusively detected during coexistence with bacteria (TB and ATB). These findings indicate that the presence of Bacillus activates cryptic biosynthetic gene clusters in Trichoderma. The antibacterial activity of mixed culture extracts was stronger than that of the monoculture extracts. The TB extract exhibited strong antifungal activity compared to the monoculture extract and other mixed culture treatments. Conclusion: The elucidation of medicinal plant microbiome interaction chemistry and its effect on the environment will also be of great interest in the context of medicinal plant health Additionally, it sheds light on the content of bioactive constituents, and facilitating the discovery of novel antimicrobials. [ABSTRACT FROM AUTHOR]

Background and aims: Wild fruit forests are vital reservoirs of germplasm genetic and biodiversity. Unfortunately, wild fruit forests of Central Asia are in the decline due to fungal disease and insect pest outbreaks. A health soil microbial community may help ameliorate the degradation of wild trees by increasing their systematic resistance, stabilizing soil carbon pool, and maintaining the quality of the habitat environment. We evaluated soil bacterial and fungal community beneath the dominant tree species, Malus sieversii (Ledeb.) M. Roem, to identify potential interactions between wild fruit forest degradation events and soil microorganisms in the Tianshan Mountain, China. Methods: Based on targeted metagenomics of the 16S rRNA and ITS (Internal Transcribed Spacer), we explored the bacterial and fungal microbial communities in soils beneath healthy and degraded M. sieversii trees (i.e., microbial biomass, species interactions, potential and niche breadth), and soil physicochemical properties. Results: We found that the degradation of M. sieversii reduced the beta diversity of topsoil bacterial communities and fungal symbiotic groups. The decline in M. sieversii abundance loosened connections within bacterial and fungal co-occurrence networks. Community assembly identified higher migration rates in the topsoil around degraded M. sieversii for bacteria and for fungi, suggesting that dispersal restricted in degraded wild fruit forest soils. Ultimately, the demise of M. sieversii homogenized the soil bacteria resulting in a narrow niche-breadth, enhanced pathogenetic fungal species, and reduced beneficial symbiotic and saprotrophic fungal diversity. Conclusions: Our results demonstrated that the degradation of M. sieversii leads to alterations in diversity, self-assembling and resource competitiveness of forest soil-dwelling microorganisms. [ABSTRACT FROM AUTHOR]

Background and aims: Forest management practices affect soil carbon dynamics, particularly by changing the diversity of aboveground plant functional groups. However, we have a limited understanding of the underlying mechanisms for how plant management affects soil respiration in planted forest ecosystems. Methods: We conducted a 3-year manipulation experiment of plant functional groups that included understory removal, tree root trenching, and fertilization treatments in 2-year-old and 6-year-old Eucalyptus plantations in the subtropical region, to explore the responses of soil carbon emission and microbial community composition. Results: Soil respiration was significantly suppressed by understory removal (-38%), tree root trenching (-41%), and their interactions (-54%), but fertilization alone and in interactions had no significant effect. Soil bacterial and fungal diversity was negatively affected by understory removal and tree root trenching, respectively. Soil respiration and microbial diversity were lower in younger plantations. Reductions in soil carbon emissions were associated with losses of plant functional groups and soil microbial diversity, while increases in soil respiration were associated with soil physicochemical factors, soil temperature, and plantation age. Conclusions: The results indicated that understory removal and tree root trenching strongly affected soil respiration, while the power effects were regulated by soil microbial community and soil properties in contrast plantation ages. Our findings highlight that plant management is of great significance to the soil carbon emission processes in afforested plantations. [ABSTRACT FROM AUTHOR]

Background and aims: Afforestation can alter belowground microbial diversity and affect soil‒plant feedback, which is crucial for understanding nutrient cycles and ecosystem productivity. Most studies have focused on the carbon and nitrogen cycles in forest ecosystems; however, there are few studies on the effect of afforestation in soil microbial diversity on phosphorus (P) nutrients. In this study, we explored the effect of soil microbial communities on soil‒plant P feedback under long-term afforestation. Methods: Typical poplar plantations were selected from the Lhasa River Basin. We assessed the P content, activity of extracellular enzyme related to P acquisition, rhizosphere soil microbes, and mechanism of microbial community. Results: Increased bacterial richness and evenness were beneficial to soil and plant P nutrition; however, the community differentiation of bacteria and fungi had no positive effect on the P content. Ecological stochasticity drove for the assembly of the rhizosphere soil microbial community after afforestation on the Tibetan Plateau. Homogenizing dispersal dominated bacterial and fungal assemblies. Ecological drift was another stochastic process that affected the microbial assembly. Conclusion: Bacterial richness and evenness had positive effects on soil‒plant P feedback, whereas microbial differentiation did not. Homogenizing dispersal and ecological drift are intrinsic factors that regulate the effects of microbial community diversity on soil‒plant P feedback processes. This study provides the evidence on the intrinsic mechanism of belowground microbial diversity influencing soil‒plant P feedback. It also provides new insights into the selection of plantation species on the Tibetan Plateau from the perspective of enhancement of P nutrition by microbes. [ABSTRACT FROM AUTHOR]

Purpose: The coastal environment is a fragile ecosystem exposed to anthropogenic pressures, including pollution. Microbial ecology studies have demonstrated the importance of microbial metabolism in marine sediments to maintain nutrient cycling; however, recalcitrant contaminants such as polycyclic aromatic hydrocarbons (PAHs) could affect these microbial communities. This study aimed to investigate the diversity of microbial communities on marine sediments from the North Occidental Coast of Baja California, Mexico (NOCBC) and their potential aromatic hydrocarbon catabolic pathways. Materials and methods: During the Southern California Bight Oceanographic Campaign, sediment samples were collected in September 2018 from 33 coastal sites from the Tijuana-San Diego border to Punta Banda Cape, Ensenada (Mexico). The samples were analyzed for grain size, total PAHs, and organic carbon (OC) concentrations. Next, the bacterial communities were identified using Illumina high-throughput sequencing of 16S rRNA genes, and hydrocarbonoclastic function was inferred using PICRUSt2. Results: According to Canadian and EPA guidelines for marine sediments, the total PAH concentration from the samples suggested a low pollution impact. Sequence analysis identified 27 phyla and 36 candidate divisions across the sampled sediments. The dominant phyla were Pseudomonadota, Bacteroidota, Planctomycetota, and Crenarchaeota. At the family level, the most prominent were Piscirickettsiaceae, OM60, Flavobacteriaceae, Pirellulaceae, and Cenarchaeaceae. The key genera were identified as Nitrosopumilus, Lutimonas, and Desulfococcus; nine Amplicon Sequence Variants (ASVs) represented the core microbiome across the sites, comprising about 7.68% of the total reads. The predictive functional analysis detected 47 principal pathways involved in hydrocarbon degradation, including catechol, protocatechuate, and aerobic toluene degradation routes. Conclusions: Our data suggest the presence of hot spots for aromatic degradative pathways in those sampling sites near cities, where a significant proportion of aromatic hydrocarbon-degrading microorganisms may be present. This study represents the first census of the prokaryotic communities from marine sediments of NOCBC, which harbors diverse communities with hydrocarbonoclastic potential. These results could provide constructive guidelines on ecosystem management and pollution mitigation actions. [ABSTRACT FROM AUTHOR]

Purpose: Mining has been carried out in San Luis Potosi, Mexico, since 1592, which has led to severe pollution issues affecting both the environment and human health. To address this, remediation projects have been initiated to restore the soil and its ecosystem services. These efforts involve removing the contaminants and restoring the soil's health and quality. This study aims to assess the biochemical impact of soil remediation carried out in the field, on areas that have been heavily contaminated with heavy metals over a prolonged period. Methods: The enzymatic activity, physiological profile, structure, and microbial diversity were used as bioindicators to assess the remediation of soil and two reference soils. Results: The results indicated that Pb and As decreased, but not at levels indicated by Mexican regulations, Cd concentrations decreased to be below Mexican regulations, the enzymatic activity between the soil with and without remediation did not present significant differences, both with low activity, arylsulfatase was the one with the highest inhibition, and urease the most activated. The evolution of the physiological activity of the microorganisms was greater in the remediated soil. Normal values of evenness and diversity were observed in soils with and without remediation, likewise, the consumption of substrates initially was towards carbohydrates and amines/amides, but in the end, carboxylic acids and polymers were consumed. Conclusion: The remediation process shows positive results; the recovery of soil health is in progress. It was demonstrated that the bioindicators used were adequate to evaluate the soil remediation process. [ABSTRACT FROM AUTHOR]

Tetracycline and copper ion are common pollutants in wastewater, and the effects of mixed pollutants on microorganisms in wastewater biological treatment have been less studied. In order to reveal the effects of mixed pollutants of tetracycline and copper ion on the microorganisms during the biological phosphorus removal, three ratios of tetracycline and copper ions were designed by the direct equipartition ray method. The relative abundance and diversity of microbial community were investigated, and the microbial interactions were revealed through microbiological methods. The results demonstrated that, for three different ratios, the inhibitory effect of specific phosphorus uptake rate became more significant with the increase of the tetracycline-copper ions concentration and the reaction time. The microbial community decreased with the increase of the proportion of tetracycline in different ratios. The relative abundance of Acinetobacter decreased with the increase of the proportion of tetracycline, while the relative abundance of Ca.Competibacter was higher under the conditions of low mixtures concentrations. Positive interactions and symbiotic relationships among microorganisms were predominant for three different ratios. However, as the proportion of tetracycline increased, the community structure of microorganisms shifted from phosphate-accumulating organisms to glycogen accumulating organisms and denitrifying bacteria. This study can provide a reference for the effect of mixed pollutants on microorganisms and the mechanism of wastewater treatment. [ABSTRACT FROM AUTHOR]

Large-scale mining activities generate significant amounts of waste that accumulates in the environment. These wastes, known as mine tailings, contain high levels of heavy metals, posing risks to human health and causing severe damage to ecosystems. In this study, we determined the heavy metal content of mine tailings in the Sierra de Huautla Biosphere Reserve (REBIOSH), Mexico, and investigated their effect on microbial composition. One of the sites historically contaminated with metals was sampled in three different locations, labeled S1, S2, and S3. A fourth site free of heavy metals (S4) was also used as a control. Our results showed high levels of As, Pb, Cd, and Ag, potentially dangerous metals that exceed thresholds set by international regulatory agencies. Metal contamination indices indicated moderate to extreme enrichment for As, Cd, and Pb, posing potential ecological risks. A metagenomic study of mine tailings showed a core specie-specific microbiome covered by Sinimarinibacterium flocculans, Jiangella anatolica, Thiobacillus denitrificans, Fontimonas thermophile, Sphingomonas koreensis. These may be associated with the processing of heavy metals. A comparative study using the ALDEx2 revealed that less represented species like Variovorax paradoxus, Usitatibacter rugosus, Usitatibacter palustris, Sphingosinicella microcystinivorans, Sphingobium yanoikuyae, and Stella humosa may serve as microbial markers in metal-contaminated environments. In addition, we detected rare or low-abundance species belonging to the phylum Armatimonadota, Candidatus Melainobacteriota, Candidatus Saccharimonadota, Chlamydiota, Deinococcota, Elusimicrobiota, Bacillota, Rhodothermota and Verrucomicrobiota, which could play an important role in ecosystems contaminated with heavy metals. Also, we found site-specific taxonomic representatives such as Nitrososphaera gargensis and Nitrospira nitrificans dominating the S3 ecosystem; Ensifer aridi (S2 and S1), N. nitrificans (S2), while Reyranella soli dominate the S1 soil. These organisms could be crucial for nitrogen access in oligotrophic environments and underscore the adaptability of microbial life to extreme conditions. This is the first comprehensive study of the microbial composition in this important ecological site of the Mexican geography and can provide future guidance for the management and biological treatment of mining wastes. [ABSTRACT FROM AUTHOR]

Aerobic granular sludge (AGS) shows promise in treating piggery wastewater compared to conventional activated sludge methods. However, current AGS research primarily remains confined to the laboratory, with limited practical applications in actual piggery wastewater treatment. Besides, AGS faces challenges such as unstable structure and susceptibility to sludge bulking in practical settings. This study aimed to assess AGS's efficacy in treating actual piggery wastewater and successfully resolved the non-filamentous bulking issue through various measures. AGS formation occurred by the 13th day of operation, demonstrating high pollutant removal rates, with ammonia nitrogen (NH4+-N), chemical oxygen demand (COD), total nitrogen (TN), and total phosphorous (TP) removal rates reaching 99%, 99%, 90%, and 96%, respectively. However, Zoogloea overgrowth led to increased polysaccharide secretion and subsequent non-filamentous bulking on the 32nd day, which adversely impacted TN, COD, and TP removal efficiency. To address the bulking issue, the influent COD concentration was initially adjusted from 500 ± 50 mg/L to 2000 ± 50 mg/L and then decreased to 700 ± 50 mg/L. Additional measures included lowering water temperature, enhancing hydraulic shear force and selective pressure, and conducting manual screening, resulting in a notable decrease in sludge bulking by the 60th day. Throughout the granulation process, there was a reduction in species diversity and microbial biomass in the sludge, especially noticeable before and after addressing the sludge bulking issue. Initially, Zoogloea dominated the AGS, but following the resolution of the non-filamentous bulking issue, there was a shift to Thauera as the dominant bacterium. [ABSTRACT FROM AUTHOR]

Deschampsia antarctica Desv. and Poa annua L. are two Poaceae plants with enough endurance to successfully establish populations in the Antarctic region. Their adaptation to the Antarctic environment is closely linked to root-associated microbial communities. In this study, we obtained 16S rRNA sequencing data of the root-associated microbial communities of these two Poaceae plants from NCBI. Meta-analysis was used to investigate the similarities and differences between the root endosphere and rhizosphere-dwelling microbial communities in these two Poaceae plants. Here we report that two Poaceae-Poaceae plants' rhizospheric communities were found to be more species diversity than endospheric communities. The species diversity of P. annua was higher than that of D. antarctica in both endosphere and rhizosphere communities. Seven bacterial families form a core microbiome of two Antarctic Poaceae plants' root endosphere, in which Microbacteriaceae appears to be obligatory root endophytes of the two Antarctic Poaceae plants. The core microbiome of the two Poaceae plants' rhizosphere has six bacterial families. Chitinophagaceae, Burkholderiaceae, and Flavobacteriaceae are most likely to play a crucial role in Poaceae plants' adaptation to cold Antarctic conditions. Sphingobacteriaceae, Caulobacteraceae, Gemmatimonadaceae, and Flavobacteriaceae have a great influence on two Antarctic Poaceae plants. [ABSTRACT FROM AUTHOR]

Mediterranean high-mountain lakes are being increasingly affected by strong Saharan dust deposition events. However, the ecological impacts of these severe atmospheric episodes remain largely unknown. We examined the effects of a strong Saharan dust intrusion to the Iberian Peninsula in 2022 on the physicochemical parameters and prokaryotic communities in sediments of nine high-mountain lakes of Sierra Nevada (Spain) located above 2800 m.a.s.l and in different orientations (north vs. south). A previous year (2021), with lower Saharan dust deposition with respect to 2022, was used for interannual comparisons. The strong dust deposition to the high-mountain lakes resulted in a significant increase in sediment nutrient availability which was linked to changes in the composition of prokaryotic communities. Decreases in alpha diversity and changes in beta diversity of prokaryotic communities were mainly observed in lakes located in the south compared to the north orientation likely because the former was more affected by the atmospheric dust deposition episode. Dust intrusion to the high-mountain lakes resulted in significant changes in the relative abundance of specific genera involved in important nutrient cycling processes such as phosphate solubilization, nitrogen fixation, nitrification, and denitrification. Saharan dust deposition also increased predicted microbial functionality in all lakes. Our findings show that severe atmospheric dust inputs to remote high-mountain lakes of Sierra Nevada can have significant biogeochemical and biodiversity consequences through changes in nutrient availability and prokaryotic communities in sediments of these freshwater ecosystems. This information contributes to understanding how Mediterranean high-mountain lakes of Sierra Nevada face strong intrusions of Saharan dust and their ecological consequences. [ABSTRACT FROM AUTHOR]

To accurately define the role of the gut microbiota in health and disease pathogenesis, the preservation of stool sample integrity, in terms of microbial community composition and metabolic function, is critical. This presents a challenge for any studies which rely on participants self-collecting and returning stool samples as this introduces variability and uncertainty of sample storage/handling. Here, we tested the performance of three stool sample collection/preservation buffers when storing human stool samples at different temperatures (room temperature [20 °C], 4 °C and – 80 °C) for up to three days. We compared and quantified differences in 16S rRNA sequencing composition and short-chain fatty acid profiles compared against immediately snap-frozen stool. We found that the choice of preservation buffer had the largest effect on the resulting microbial community and metabolomic profiles. Collectively analysis confirmed that PSP and RNAlater buffered samples most closely recapitulated the microbial diversity profile of the original (immediately – 80 °C frozen) sample and should be prioritised for human stool microbiome studies. [ABSTRACT FROM AUTHOR]

Huanglongbing, also known as citrus greening, is currently the most devastating citrus disease with limited success in prevention and mitigation. A promising strategy for Huanglongbing control is the use of antimicrobials fused to a carrier protein (phloem protein of 16 kDa or PP16) that targets vascular tissues. This study investigated the effects of genetically modified citrus trees expressing Citrus sinensis PP16 (CsPP16) fused to human lysozyme and β-defensin-2 on the soil microbiome diversity using 16S amplicon analysis. The results indicated that there were no significant alterations in alpha diversity, beta diversity, phylogenetic diversity, differential abundance, or functional prediction between the antimicrobial phloem-overexpressing plants and the control group, suggesting minimal impact on microbial community structure. However, microbiota diversity analysis revealed distinct bacterial assemblages between the rhizosphere soil and root environments. This study helps to understand the ecological implications of crops expressing phloem-targeted antimicrobials for vascular disease management, with minimal impact on soil microbiota. [ABSTRACT FROM AUTHOR]

The benefits of urban green space are socially widely recognized as a direct link between plant–microbe interactions and the maintenance of biodiversity, community stability, and ecosystem functioning. Nevertheless, there is a lack of knowledge about the factors influencing microbial communities in urban green spaces, especially those related to phyllosphere epiphytes and stem epiphytes. In this study, we analyzed the microbial community assembly in leaf and stem bark samples collected from Square, Road, Campus, and Park. Illumina sequecing of 16S amplicons was performed to characterize microbial diversity and composition. The α-diversity was significantly higher in the bark epiphytic community, compared to the phyllosphere. Moreover, urban greenspaces'type altered the way communities gathered. The main soil and air properties factors of the urban greenhouse (e.g. soil temperature, atmospheric moisture, air temperature) were shaping the characteristics of bacterial communities on the leaf surface and bark epiphytic. In addition, in the co-occurrence network analysis, keystone taxa were not mostly observed in abundant species, which may be necessary to maintain ecosystem functions. Finally, our findings provide a deeper understanding of the ecological dynamics and microbial interactions within plant phyllosphere and stem epiphytes microbiomes. [ABSTRACT FROM AUTHOR]

Background and aims: Dominant plants shape belowground communities, which in turn influences ecosystem functioning. Similarly, herbivores affect belowground communities through physical disturbance and redistribution of organic inputs, but also through their interactions with plants themselves. However, we know little about how grazing moderates the effects of dominant plants on belowground organisms. Methods: We established a three-year shrub removal experiment in a grazed and an ungrazed alpine meadow on the Qinghai-Tibet plateau to assess how grazing moderates the effects of a dominant plant, Dasiphora fruticosa, on nematode communities. We used piecewise structural equation modelling to assess how grazing moderates the direct effects of dominant plants and, indirect effects via changes in edaphic variables and microbial pathways. Results: We found that 1) grazing significantly decreased nematode diversity mainly due to a reduction in omnivores; 2) there was a significant grazing by shrub interaction effect on nematode diversity, whereby shrub had a positive direct effect on nematode diversity only in the grazed meadow; 3) in the ungrazed alpine meadow, microbial diversity was a strong predictor of nematode, while in the grazed meadow, grazing suppressed the microbial pathways of shrub presence. Conclusion: The study shows that grazing decreases the diversity of soil communities and suppresses the interactions among soil biota, while shrub presence plays a vital role in alleviating the negative effects of grazing on understory communities. Therefore, the findings further highlight herbivory in inducing facilitation of dominant shrubs on understory community stabilization and ecosystem functioning in alpine meadows of the Qinghai-Tibetan plateau. [ABSTRACT FROM AUTHOR]

Background: Soil microbial community composition with stand development may be changed due to the variations in canopy structure, understory vegetation, root traits, edaphic conditions, and litter inputs. However, it is still uncertain to what extent these biotic and abiotic factors shape the soil microbial community composition in Chinese fir (Cunninghamia lanceolata) plantations, which are widely planted in southern China. Methods: Amplicon sequencing was used to analyze the diversity and composition of soil bacterial and fungal communities at two soil depths across four developmental stages of Chinese fir plantations. Results: Both the bacterial and fungal communities were significantly different between stand age groups. As stand aged, oligotrophic bacteria decreased in abundance while copiotrophic bacteria increased. Meanwhile, fungal functional groups connected to plants decreased in abundance while that of saprotrophic fungi significantly increased. The variance in bacterial community was mainly attributed to soil variables regarding carbon and nutrient availability, whereas the greatest fraction of fungal community dissimilarity was determined by plant-specific factors such as aboveground stand structure and tree root traits. The chemical composition of litter had a major effect on the soil fungal community, whereas the litter traits had no effect on the bacterial community. Conclusions: The potential drivers of soil fungi and bacteria differ in Chinese fir plantations. By accounting for the impacts of various environmental components, it is possible to anticipate the response of soil bacterial and fungal assemblages to forest management regime implemented in Chinese fir plantations. [ABSTRACT FROM AUTHOR]

Background and aims: The diversity and stability of belowground microbiota communities influence plant health. However, changes over time in the microbiome composition associated with healthy and diseased trees remains poorly understood. The goal of this study is to understand the changes in belowground microbial community associated with Verticillium wilt of smoke trees to provide a basis for the combination of biological agents and chemical measures to combat Verticillium wilt of smoke trees. Methods: In this study, we used an amplicon-based approach to reveal distinct differences in the diversity, structure and composition of the belowground microbial communities of healthy and diseased smoke trees from June to October. Results: The structure, composition and interactions of the belowground microbial communities are different between healthy and diseased smoke trees from June to October. The co-occurrence networks of the belowground microbial community changed with the severity of the disease over time. Additionally, the structural community of healthy and diseased trees showed a shift in keystone OTUs. Conclusions: This study improves our understanding of the belowground microbial community composition associated with smoke trees in healthy and diseased conditions, offering the potential to both manipulate the plant microbiome to promote plant health and to provide an integrated management strategy of smoke tree. [ABSTRACT FROM AUTHOR]

Background: Land degradation and climate change pose serious threats to global biodiversity and ecosystem functions and services. The key role of plant diversity in resisting the negative impacts of disturbances and restoring degraded ecosystems has been well documented. Recent evidence has also highlighted the critical roles of soil microbial diversity. However, mechanistic knowledge and field evidence of soil biodiversity in restoration remain limited. Developing an improved understanding of how soil biodiversity responds and resists to environmental disturbances, particularly the combined effects of multiple disturbances, can provide critical mechanistic knowledge to develop effective restoration tools. Scope: In this article, we provide a brief overview of recent advancements in our understanding of the impacts of land degradation and climate change on soil microbial diversity and ecosystem functions and services. Further, we identify the main knowledge gaps, propose new concepts, and make recommendations for future research directions. Specifically, we propose a new concept that combine multiple ecological theories (e.g., meta-community, invasion, and coalescence) and suggest that both plant and soil biodiversity, as well as their interactions, be explicitly considered to improve mechanistic understanding of the resistance and resilience of ecosystems to increasing disturbances. Adopting a framework that combines both plant and soil biodiversity approaches is likely provide improved ecosystem restoration outcomes. Conclusions: We advocate for a systems-based approach to ecosystem restoration that integrates biological approaches with environmental variables (e.g., ecosystem properties, climatic conditions, and soil types). To support this approach, we propose the integration of new computational and satellite tools that have the potential to facilitate the implementation of better management, monitoring, and restoration of ecosystems. [ABSTRACT FROM AUTHOR]

Aims and background: The resurrection plant Myrothamnus flabellifolia tolerates complete desiccation and is a great model for studying how plants cope with extreme drought. Root-associated microbes play a major role in stress tolerance and are an attractive target for enhancing drought tolerance in staple crops. However, how these dynamics play out under the most extreme water limitation remains underexplored. This study aimed to identify bacterial and fungal communities that tolerate extreme drought stress in the bulk soil, rhizosphere, and endosphere of M. flabellifolia. Methods: High-throughput amplicon sequencing was used to characterise the microbial communities associated with M. flabellifolia. Results: The bacterial phyla that were most abundant across all compartments were Acidobacteriota, Actinobacteriota, Chloroflexota, Planctomycetota, and Pseudomonadota, while the most abundant fungal phyla were Ascomycota and Basidiomycota. Although the bulk soil hosted multiple beneficial root-associated microbes, the rhizosphere compartment showed the highest functional diversity of bacteria and fungi. In contrast, the endosphere exhibited a low abundance and diversity of microbes. These findings share consistent with the theory that M. flabellifolia recruits soil microbes from the bulk to the rhizosphere and finally to the endosphere. It is possible that these microbes could promote drought tolerance in associated plant tissues. Conclusion: We find that compartments act as the major driver of microbial diversity, but the soil physicochemical factors also influence microbial composition. These results suggest that the root-associated microbiome of M. flabellifolia is highly structured and may aid in plant function. [ABSTRACT FROM AUTHOR]

Purpose: Soil quality is crucial for the growth and development of tea plants. Although the tea rhizosphere microbial composition and function have been extensively studied, few comparative studies have been performed to explore the different ecological niches of tea plants' microbes and their response to current global warming. Materials and methods: In this study, we selected a typical tea plant soil located in Chibi city, Hubei Province, China and collected samples during different seasons from rhizosphere and nonrhizosphere of tea plants. Using the Microbial phospholipid fatty acid analysis method and high-throughput sequencing to analyze the functions of dominant bacterial communities and strategies for coping with different environmental pressures. Results and discussion: The results showed that 19:0 cyclo ω7c was the dominant peak in both the rhizosphere and nonrhizosphere environments in winter compared with 16:0 in both the rhizosphere and nonrhizosphere soil in summer. The composition of PLFAs and a series of derived parameters were regulated by environmental factors such as soil pH, redox potential, total organic carbon, total nitrogen and NO3−-N content. In addition, the tea plant soil microorganisms differed significantly under the different temperature stresses, with significant enrichment of Ktedonobacteria and Micrococcaceae in winter and of Gammaproteobacteria and Proteobacteria in summer. Conclusions: The rhizosphere and nonrhizosphere soil microbial communities of tea plants were co-regulated by the root secretions growth conditions of tea plants, the fertilization conditions and the temperature stress. [ABSTRACT FROM AUTHOR]

Aquaculture plays a vital role in meeting global food demand, and shrimp farming is a major contributor to this industry. Despite the immense economic importance of farmed shrimp, disease outbreaks continue to pose a significant challenge. This was attributed to fluctuations in various biotic and abiotic factors such as temperature, salinity, nutrition absorption, and water quality, which favor the abundance of invaders or opportunistic pathogens. Furthermore, the alterations in the gut microbiota, particularly decreased levels of commensals and increased prevalence of pathogens were reported during disease outbreaks. Shrimp physiology and immune function are intimately intertwined with the gut microbiome, leading to a dynamic interplay where the host shapes the microbial community through selection, while the microbes in turn influence the host's metabolism and immune responses. Although various literatures report the change in gut microbial diversity and the immune responses generated by the host against various pathogens, a crucial knowledge gap exists regarding the intricate communication between these two systems. This review bridges this gap by deciphering the intricate interplay between host immunity and gut microbes, elucidating on the mechanisms underlying successful shrimp disease establishment. Thus, this review could offer possibilities for generating ideas to carry out effective aquaculture practices. [ABSTRACT FROM AUTHOR]

In the present study, the evolution of the physicochemical and microbiological characteristics of lactic acid bacteria (LAB) in traditional Kırklareli white brined cheese collected from 14 different cheese manufacturing facilities were investigated on different days of the 90-day ripening period. The obtained LAB within the species Lactococcus (Lc.) lactis, Latilactobacillus (Lt.) curvatus, Lactobacillus (Lb.) casei and Lb. plantarum, Enterococcus (E.) durans, E. faecium, E. faecalis, Streptococcus macedonicus, and Weissella paramesenteroides were characterized in terms of their influence on technological properties and their potential as starter cultures for traditional white brined cheese production. The results of the microbiological and physicochemical investigations showed that a few selected isolates of Lc. lactis, Lb. casei, and Lb. plantarum had certain functions as starter germs. Moderate acidification capacity, antibacterial activity and proteolytic activity, which are characteristic of their use as starter lactic acid bacteria, were found. Importantly, antibiotic resistance among selected Lc. lactis, Lb. casei, and Lb. plantarum isolates was extremely low, whereas some of these isolates demonstrated antibacterial activity against major foodborne pathogenic bacteria. Based on the results obtained in this study, selected Lc. and Lb. isolates can also be considered as starter culture in traditional cheese production. [ABSTRACT FROM AUTHOR]

Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15–20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change. [ABSTRACT FROM AUTHOR]

Despite recent research efforts to explore the co-occurrence patterns of diverse microbes within soil microbial communities, a substantial knowledge-gap persists regarding global climate influences on soil microbiota behaviour. Comprehending co-occurrence patterns within distinct geoclimatic groups is pivotal for unravelling the ecological structure of microbial communities, that are crucial for preserving ecosystem functions and services. Our study addresses this gap by examining global climatic patterns of microbial diversity. Using data from the Earth Microbiome Project, we analyse a meta-community co-occurrence network for bacterial communities. This method unveils substantial shifts in topological features, highlighting regional and climatic trends. Arid, Polar, and Tropical zones show lower diversity but maintain denser networks, whereas Temperate and Cold zones display higher diversity alongside more modular networks. Furthermore, it identifies significant co-occurrence patterns across diverse climatic regions. Central taxa associated with different climates are pinpointed, highlighting climate's pivotal role in community structure. In conclusion, our study identifies significant correlations between microbial interactions in diverse climatic regions, contributing valuable insights into the intricate dynamics of soil microbiota. [ABSTRACT FROM AUTHOR]

Understanding the extent of heritability of a plant-associated microbiome (phytobiome) is critically important for exploitation of phytobiomes in agriculture. Two crosses were made between pairs of cotton cultivars (Z2 and J11, L1 and Z49) with differential resistance to Verticillium wilt. F2 plants were grown in a field, together with the four parents to study the heritability of cotton rhizosphere microbiome. Amplicon sequencing was used to profile bacterial and fungal communities in the rhizosphere. F2 offspring plants of both crosses had higher average alpha diversity indices than the two parents; parents differed significantly from F2 offspring in Bray–Curtis beta diversity indices as well. Two types of data were used to study the heritability of rhizosphere microbiome: principal components (PCs) and individual top microbial operational taxonomic units (OTUs). For the L1 × Z49 cross, the variance among the F2 progeny genotypes (namely, genetic variance, VT) was significantly greater than the random variability (VE) for 12 and 34 out of top 100 fungal and bacterial PCs, respectively. For the Z2 × J11 cross, the corresponding values were 10 and 20 PCs. For 29 fungal OTUs and 10 bacterial OTUs out of the most abundant 100 OTUs, genetic variance (VT) was significantly greater than VE for the L1 × Z49 cross; the corresponding values for the Z2 × J11 cross were 24 and one. The estimated heritability was mostly in the range of 40% to 60%. These results suggested the existence of genetic control of polygenic nature for specific components of rhizosphere microbiome in cotton. Key points: • F2offspring cotton plants differed significantly from parents in rhizosphere microbial diversity. • Specific rhizosphere components are likely to be genetically controlled by plants. • Common PCs and specific microbial groups are significant genetic components between the two crosses. [ABSTRACT FROM AUTHOR]

When antimicrobial resistant bacteria (ARB) and genes (ARGs) reach novel habitats, they can become part of the habitat's microbiome in the long term if they are able to overcome the habitat's biotic resilience towards immigration. This process should become more difficult with increasing biodiversity, as exploitable niches in a given habitat are reduced for immigrants when more diverse competitors are present. Consequently, microbial diversity could provide a natural barrier towards antimicrobial resistance by reducing the persistence time of immigrating ARB and ARG. To test this hypothesis, a pan-European sampling campaign was performed for structured forest soil and dynamic riverbed environments of low anthropogenic impact. In soils, higher diversity, evenness and richness were significantly negatively correlated with relative abundance of >85% of ARGs. Furthermore, the number of detected ARGs per sample were inversely correlated with diversity. However, no such effects were present in the more dynamic riverbeds. Hence, microbiome diversity can serve as a barrier towards antimicrobial resistance dissemination in stationary, structured environments, where long-term, diversity-based resilience against immigration can evolve. A study based on a pan-European survey of soils and riverbeds of low-anthropogenic impact suggests that environmental microbiomes with a higher degree of bacterial diversity host less diverse and lower abundances of antibiotic resistance genes. [ABSTRACT FROM AUTHOR]

Background: Mixed forests are better than monoculture forests in biodiversity, stand structure and productivity stability. However, a more comprehensive assessment of the ecosystem functions of monoculture and mixed plantations is lacking. We compared the single functions and ecosystem multifunctionality (EMF) in Fraxinus mandshurica and Larix olgensis mixed plantations with monoculture plantations in Northeast China and discussed the influences of biodiversity and environmental factors on EMF. Results: The mixed plantations had higher biodiversity and ecological functions. Biodiversity was significantly higher in mixed plantations (such as CWMMH, Shrub.Shannon, Shrub.Richness, Herb.Shannon, Herb.Richness), but environmental factors differed less among the three forest types, and below ground diversity differed significantly only in the Bacterial.Shannon and Fungal.Shannon. Mixed plantations showed significant differences in single ecological functions relative to monoculture plantations, with more pronounced differences between mixed plantations and Larix olgensis monoculture plantations. Weighted ecosystem multifunctionality was significantly higher in mixed plantations than in monoculture plantations. EMF was mainly driven by tree diversity, environmental factors, shrub and herb species diversity, and soil microbial alpha diversity, which explained 25.35%, 8.94%, 8.83%, and 7.65% of the variation, respectively. Conclusions: The establishment of mixed plantations can increase the biodiversity of forest stands and improve the ecosystem functions. These results highlight the advantages of multi-species plantations and the necessity of planting them. They are important for the conservation of biodiversity and the sustainable management of plantations. [ABSTRACT FROM AUTHOR]

Denitrification and anaerobic ammonium oxidation (anammox) are key processes for nitrogen removal in aquaculture, reducing the accumulated nitrogen nutrients to nitrogen gas or nitrous oxide gas. Complete removal of nitrogen from aquaculture systems is an important measure to solve environmental pollution. In order to evaluate the nitrogen removal potential of marine aquaculture ponds, this study investigated the denitrification and anammox rates, the flux of nitrous oxide (N2O) at the water–air interface, the sediment microbial community structure, and the gene expression associated with the nitrogen removal process in integrated multi-trophic aquaculture (IMTA) ponds (Apostistius japonicus-Penaeus japonicus-Ulva) with different culture periods. The results showed that the denitrification and anammox rates in sediments increased with the increase of cultivation periods and depth, and there was no significant difference in nitrous oxide gas flux at the water–air interface between different cultivation periods (p > 0.05). At the genus and phylum levels, the abundance of microorganisms related to nitrogen removal reactions in sediments changed significantly with the increase of cultivation period and depth, and was most significantly affected by the concentration of particulate organic nitrogen (PON) in sediments. The expression of denitrification gene (narG, nirS, nosZ) in surface sediments was significantly higher than that in deep sediments (p < 0.05), and was negatively correlated with denitrification rate. All samples had a certain anammox capacity, but no known anammox bacteria were found in the microbial diversity detection, and the expression of gene (hzsB) related to the anammox process was extremely low, which may indicate the existence of an unknown anammox bacterium. The data of this study showed that the IMTA culture pond had a certain potential for nitrogen removal, and whether it could make a contribution to reducing the pollution of culture wastewater still needed additional practice and evaluation, and also provided a theoretical basis for the nitrogen removal research of coastal mariculture ponds. [ABSTRACT FROM AUTHOR]

Current knowledge about effects of disturbance on the fate of invaders in complex microbial ecosystems is still in its infancy. In order to investigate this issue, we compared the fate of Klebsiella pneumoniae (Kp) and Listeria monocytogenes (Lm) in soil microcosms. We then used environmental disturbances (freeze–thaw or heat cycles) to compare the fate of both invaders and manipulate soil microbial diversity. Population dynamics of the two pathogens was assessed over 50 days of invasion while microbial diversity was measured at times 0, 20 and 40 days. The outcome of invasion was strain-dependent and the response of the two invaders to disturbance differed. Resistance to Kp invasion was higher under the conditions where resident microbial diversity was the highest while a significant drop of diversity was linked to a higher persistence. In contrast, Lm faced stronger resistance to invasion in heat-treated microcosms where diversity was the lowest. Our results show that diversity is not a universal proxy of resistance to microbial invasion, indicating the need to properly assess other intrinsic properties of the invader, such as its metabolic repertoire, or the array of interactions between the invader and resident communities. [ABSTRACT FROM AUTHOR]

Microorganisms capable of degrading hydrocarbons are regular components of natural microbial communities and play an important role in self-purification of marine environments from oil contamination. High-throughput sequencing of the 16S rRNA gene V4 variable region was used to analyze microbial communities of the Barents and Pechora seas and of the microcosms with a spectrum of hydrocarbon substrates: oil, n-nonane, n-undecane, and phenanthrene. The Barents Sea communities of hydrocarbon-oxidizing microorganisms were characterized by the predominance of the genera Pseudoalteromonas, Pseudomonas, Porticoccus, and Oleispira, while those of the Pechora Sea contained members of the genera Rhodococcus, Dietzia, Sphingorhabdus, and Hyphomonas. Pure cultures of these microorganisms were shown to utilize the major oil hydrocarbons: n-alkanes, cycloalkanes, and aromatic compounds. [ABSTRACT FROM AUTHOR]